BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240035.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 1,710,089 number of mapped reads = 1,354,833 (79.23%) number of supplementary alignments = 5,070 (0.3%) number of secondary alignments = 0 number of mapped bases = 82,267,833 bp number of sequenced bases = 82,218,168 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,070 duplication rate = 7.49% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4068 >>>>>>> ACTG content number of A's = 21,929,445 bp (26.67%) number of C's = 13,998,097 bp (17.03%) number of T's = 27,087,740 bp (32.95%) number of G's = 19,145,771 bp (23.29%) number of N's = 57,115 bp (0.07%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0103 number of mismatches = 837,056 number of insertions = 5,789 mapped reads with insertion percentage = 0.42% number of deletions = 29,287 mapped reads with deletion percentage = 2.14% homopolymer indels = 50.71% >>>>>>> Coverage mean coverageData = 0.0266X std coverageData = 0.2763X There is a 2.04% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6144628 0.024652407987380703 0.3600493292353286 chr2 243199373 8564969 0.03521789096059882 0.30479866912683334 chr3 198022430 5860228 0.029593758646432124 0.21864462093231501 chr4 191154276 5508013 0.028814490134659608 0.21946612886329825 chr5 180915260 4372199 0.02416711006025694 0.19642973275195447 chr6 171115067 4559818 0.02664767094998128 0.23706847084797447 chr7 159138663 5390018 0.03386994648811396 0.5857005784186721 chr8 146364022 5189251 0.03545441652320814 0.33163308217767207 chr9 141213431 2992583 0.02119191481155925 0.2364155139568872 chr10 135534747 3575237 0.026378748469571424 0.23252433533528322 chr11 135006516 3694790 0.027367493877110346 0.24794844793225818 chr12 133851895 3692624 0.027587386790452237 0.20944799285735582 chr13 115169878 1884331 0.01636131801754622 0.1616293888019843 chr14 107349540 2852598 0.026572987643915382 0.21466226707048466 chr15 102531392 2095023 0.020432990902922686 0.18928216864228758 chr16 90354753 2178982 0.02411585365077585 0.19583197503999175 chr17 81195210 2216409 0.02729728761093173 0.22275971757874719 chr18 78077248 1841634 0.023587332381387213 0.3160646877359165 chr19 59128983 1391192 0.023528089431201615 0.27562233159449306 chr20 63025520 1635548 0.025950567325743603 0.20433035743636085 chr21 48129895 1334913 0.027735630838172407 0.21507731160160856 chr22 51304566 775550 0.01511658825844078 0.15061660609522035 chrMT 16571 48577 2.9314465029268 4.286726866005567 chrX 155270560 4297366 0.027676631036817282 0.22349381231275972 chrY 59373566 171352 0.002885998122464128 0.06731479155738695